Tag: kegg
KEGG ORTHOLOGY: K06625
Brite KEGG Orthology (KO) [BR:ko00001] 09130 Environmental Information Processing 09132 Signal transduction 04012 ErbB signaling pathway K06625 CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A 04630 JAK-STAT signaling pathway K06625 CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A 04066 HIF-1 signaling pathway K06625 CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A 04068 FoxO signaling pathway K06625 CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A 04151 PI3K-Akt signaling pathway K06625 CDKN1A, P21,…
KEGG COMPOUND: C05924
KEGG COMPOUND: C05924 COMPOUND: C05924 Help Entry C05924 Compound Name Molybdopterin;Pyranopterin;H2Dtpp-mP Formula C10H14N5O6PS2 Exact mass 395.0123 Mol weight 395.3518 Structure Mol fileKCF fileDB search Reaction Pathway Module M00880 Molybdenum cofactor biosynthesis, GTP => molybdenum cofactor Enzyme Other DBs KCF data Show ATOM 24 1 S1a S 22.7500 -13.4003 2 S1a S 25.1308 -14.8087 3 C2y C 22.7383 -14.7666 4 C2y C 23.9353 -15.4866 5 C1y C 21.5555 -15.4809 6 C1y C 23.9236 -16.8776 7 C1y C 21.5496 -16.8718 8 N1x N 20.3269 -14.7608 9 C1b…
MND1 Expression as a Predictor of Breast Cancer Survival
Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…
Role of CD68 in tumor immunity and prognosis prediction in pan-cancer
Expression of CD68 in pan-cancer First, to fully clarify the expression of CD68 in pan-cancer, we matched the GTEx normal samples with TCGA tumor samples (Fig. 1A). We found that the levels of CD68 were significantly elevated (P < 0.01) in colon adenocarcinoma (COAD), glioblastoma multiforme (GBM), kidney renal clear cell carcinoma (KIRC),…
Circulating cell-free mtDNA release is associated with the activation of cGAS-STING pathway and inflammation in mitochondrial diseases
Craven L, Alston C, Taylor R, Turnbull D (2017) Recent advances in mitochondrial disease. Annu Rev Genomics Hum Genet 18:257–275. doi.org/10.1146/annurev-genom-091416-035426 CAS Article PubMed Google Scholar El-Hattab AW, Adesina AM, Jones J, Scaglia F (2015) MELAS syndrome: clinical manifestations, pathogenesis, and treatment options. Mol Genet Metab 116(1–2):4–12. doi.org/10.1016/j.ymgme.2015.06.004 CAS Article …
Differential Expression Profiles and Bioinformatics Analysis of tRNA-Derived Small RNAs in Muscle-Invasive Bladder Cancer in a Chinese Population
This article was originally published here Genes (Basel). 2022 Mar 28;13(4):601. doi: 10.3390/genes13040601. ABSTRACT Muscle-invasive bladder cancer (MIBC) leads to a large societal burden. Recently, tRNA-derived small RNAs (tsRNAs), a novel type of noncoding RNA (ncRNAs), have been identified. However, the expression patterns and functions of tsRNAs in MIBC have…
KEGG COMPOUND: C05345
KEGG COMPOUND: C05345 COMPOUND: C05345 Help Entry C05345 Compound Name beta-D-Fructose 6-phosphate;beta-D-Fructofuranose 6-phosphate Formula C6H13O9P Exact mass 260.0297 Mol weight 260.1358 Structure Mol fileKCF fileDB search Reaction Pathway map00010 Glycolysis / Gluconeogenesis map00051 Fructose and mannose metabolism map00520 Amino sugar and nucleotide sugar metabolism map00541 O-Antigen nucleotide sugar biosynthesis map00997 …
Construction of a circRNA-Mediated ceRNA Network Reveals Novel Biomarkers for Aortic Dissection
Background: Aortic dissection (AD) is a rare and lethal disorder with its genetic basis remains largely unknown. Many studies have confirmed that circRNAs play important roles in various physiological and pathological processes. However, the roles of circRNAs in AD are still unclear and need further investigation. The present study aimed…
KEGG MODULE: M00567
MODULE: M00567 Help Entry M00567 Pathway Module Name Methanogenesis, CO2 => methane Definition (K00200+K00201+K00202+K00203-K11261+(K00205,K11260,K00204)) K00672 K01499 (K00319,K13942) K00320 (K00577+K00578+K00579+K00580+K00581-K00582-K00583+K00584) (K00399+K00401+K00402) (K22480+K22481+K22482,K03388+K03389+K03390,K08264+K08265,K03388+K03389+K03390+K14127+(K14126+K14128,K22516+K00125)) Diagram Orthology 4Fe-4S ferredoxin formylmethanofuran–tetrahydromethanopterin N-formyltransferase [EC:2.3.1.101] [RN:R03390] methenyltetrahydromethanopterin cyclohydrolase [EC:3.5.4.27] [RN:R03464] methylenetetrahydromethanopterin dehydrogenase [EC:1.5.99.9] [RN:R04456] 5,10-methenyltetrahydromethanopterin hydrogenase [EC:1.12.98.2] [RN:R04455] coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase [EC:1.5.99.11] [RN:R04464] Ortholog tableTaxonomyModule table…
N6-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance | Military Medical Research
Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…
A hypoxia-related signature in lung squamous cell carcinoma
Introduction Lung cancer is the major leading cause of tumour-related deaths throughout the world, while lung squamous cell carcinoma (LUSC) as the second most common histological type of lung cancer.1 Each year, almost 1.8 million people are diagnosed with lung cancer worldwide and 400,000 of these die from LUSC.2,3 Due to…
Bioconductor – keggorthology
This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see keggorthology. graph support for KO, KEGG Orthology Bioconductor version: 2.13 graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused…
Bioconductor – neaGUI
This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see neaGUI. An R package to perform the network enrichment analysis (NEA). Bioconductor version: 2.13 neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko…
Bioinformatics analysis identifies widely expressed genes
1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…
A multi-omics approach to elucidate the mechanisms of action of a dietary muramidase administered to broiler chickens
Gadde, U., Kim, W. H., Oh, S. T. & Lillehoj, H. S. Alternatives to antibiotics for maximizing growth performance and feed efficiency in poultry: a review. Animal Health Res. Rev. 18, 26–45 (2017). CAS Google Scholar Smits, C. H. M., Li, D., Patience, J. F. & den Hartog, L. A….
Metagenomic data-analysis reveals enrichment of lipopolysaccharide synthesis in the gut microbiota of atrial fibrillation patients
This article was originally published here Zhonghua Xin Xue Guan Bing Za Zhi. 2022 Mar 24;50(3):249-256. doi: 10.3760/cma.j.cn112148-20210106-00015. ABSTRACT Objective: To investigate the functional changes of key gut microbiota (GM) that produce lipopolysaccharide (LPS) in atrial fibrillation (AF) patients and to explore their potential role in the pathogenesis of AF….
KEGG COMPOUND: C01380
Entry C01380 Compound Name Ethylene glycol;1,2-Ethanediol;Ethane-1,2-diol Formula C2H6O2 Exact mass 62.0368 Mol weight 62.0678 Structure Mol fileKCF fileDB search Reaction Pathway map00625 Chloroalkane and chloroalkene degradation map00630 Glyoxylate and dicarboxylate metabolism map01120 Microbial metabolism in diverse environments Enzyme Other DBs KCF data Show ATOM 4 1 C1b C 28.1392 -16.3327 2 C1b C 29.5408 -16.3327 3 O1a O 27.4444 -17.5473 4 O1a O 30.2356 -17.5473BOND 3 1 1 2 1 2 1 3 1 3 2 4 1…
Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis
Rawla, P., Sunkara, T., Muralidharan, P. & Raj, J. P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Poznan, Poland) 22, 141–150 (2018). CAS Google Scholar Kong, D. et al. Current statuses of molecular targeted and immune checkpoint therapies in hepatocellular carcinoma. Am. J. Cancer Res. 10,…
KEGG REACTION: R01627
KEGG REACTION: R01627 REACTION: R01627 Help Entry R01627 Reaction Name 3-dehydroshikimate hydro-lyase Definition 3-Dehydroshikimate <=> 3,4-Dihydroxybenzoate + H2O Equation Reaction class Enzyme Pathway rn01053 Biosynthesis of siderophore group nonribosomal peptides rn01110 Biosynthesis of secondary metabolites Orthology Other DBs LinkDB All DBs DBGET integrated database retrieval system Read more here: Source…
KEGG COMPOUND: C02538
KEGG COMPOUND: C02538 COMPOUND: C02538 Help Entry C02538 Compound Name Formula C18H22O5S Exact mass 350.1188 Mol weight 350.4293 Structure Mol fileKCF fileDB search Reaction Pathway map00140 Steroid hormone biosynthesis Enzyme Brite Compounds with biological roles [BR:br08001] Hormones and transmitters Steroid hormones Estrogens C02538 Estrone 3-sulfateLipids [BR:br08002] ST Sterol lipids ST02 Steroids ST0201 C18 steroids (estrogens) and derivatives C02538 Estrone 3-sulfate ST05 Steroid…
Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation
Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…
Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis
Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS PubMed Google Scholar Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…
KEGG ORTHOLOGY: K13942
KEGG ORTHOLOGY: K13942 ORTHOLOGY: K13942 Help Entry K13942 KO Symbol hmd Name 5,10-methenyltetrahydromethanopterin hydrogenase [EC:1.12.98.2] Pathway map01120 Microbial metabolism in diverse environments Module M00567 Methanogenesis, CO2 => methane Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism 09102 Energy metabolism 00680 Methane metabolism K13942 hmd; 5,10-methenyltetrahydromethanopterin hydrogenaseEnzymes [BR:ko01000] 1. Oxidoreductases 1.12 Acting on hydrogen as donor 1.12.98 With other, known, physiological acceptors 1.12.98.2 5,10-methenyltetrahydromethanopterin…
Efficient way of mapping UniProt IDs to representative UniRef90 IDs?
You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…
Identification of Hub Genes Associated with COPD Through Integrated Bi
Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…
KEGG COMPOUND: C01113
KEGG COMPOUND: C01113 COMPOUND: C01113 Help Entry C01113 Compound Name D-Galactose 6-phosphate;6-Phospho-D-galactose Formula C6H13O9P Exact mass 260.0297 Mol weight 260.1358 Structure Mol fileKCF fileDB search Reaction Pathway map02060 Phosphotransferase system (PTS) Enzyme Other DBs KCF data Show ATOM 16 1 P1b P 25.9015 -16.0011 2 O2b O 27.3009 -16.0070 3 O1c O 25.8898 -17.4005 4 O1c O 24.5021 -16.0011 5 O1c O 25.8898 -14.6076 6 C1b C 28.3679 -15.0973 7 C1y C 29.5748 -15.8029 8 C1y C 29.5748 -17.2021 9 O2x O 30.7818 -15.0973 10 C1y C 30.7818 -17.9018 11 O1a O 28.3679 -17.9018 12 C1y C 32.0005 -15.8029 13 C1y…
KEGG COMPOUND: C00469
KEGG COMPOUND: C00469 COMPOUND: C00469 Help Entry C00469 Compound Name Ethanol;Ethyl alcohol;Methylcarbinol Formula C2H6O Exact mass 46.0419 Mol weight 46.0684 Structure Mol fileKCF fileDB search Remark Reaction Pathway map00010 Glycolysis / Gluconeogenesis map01110 Biosynthesis of secondary metabolites map01120 Microbial metabolism in diverse environments map04750 Inflammatory mediator regulation of TRP channels…
KEGG T01001: 5105
Entry 5106 CDS T01001 Symbol PCK2, PEPCK, PEPCK-M, PEPCK2 Name (RefSeq) phosphoenolpyruvate carboxykinase 2, mitochondrial KO K01596 phosphoenolpyruvate carboxykinase (GTP) [EC:4.1.1.32] Organism hsa Homo sapiens (human) Pathway hsa00010 Glycolysis / Gluconeogenesis hsa00020 Citrate cycle (TCA cycle) hsa00620 Pyruvate metabolism hsa01100 Metabolic pathways hsa03320 PPAR signaling pathway hsa04068 FoxO signaling pathway hsa04151 PI3K-Akt signaling…
KEGG COMPOUND: C00565
Entry C00565 Compound Name Trimethylamine;(CH3)3N;N,N-Dimethylmethanamine Formula C3H9N Exact mass 59.0735 Mol weight 59.1103 Structure Mol fileKCF fileDB search Reaction Pathway map01120 Microbial metabolism in diverse environments Module M00563 Methanogenesis, methylamine/dimethylamine/trimethylamine => methane Enzyme Other DBs KCF data Show ATOM 4 1 N1c N 22.1200 -15.8200 2 C1a C 23.3299 -15.1185 3 C1a C 20.9101 -15.1185 4 C1a C 22.1200 -17.2929BOND 3 1 1 2 1 2 1 3 1 3 1 4 1 Read more here: Source link
Workflow Platforms for Systems Genetics
Workflow Platforms for Systems Genetics eQTL Platforms eQTL Viewer Mouse Genome Informatics: Phenotypes, Alleles & Disease Models PhenoGen Informatics (CO U) eXtensible Genotype And Phenotype platform (XGAP) MOLGENIS & MetaNetwork, Swertz & Jansen, U Groningen Weighted Gene Co-expression Network Analysis (WGCNA), Horvath, UCLA iPlant Sage Bionetworks Repository: Synapse GenomeSpace Institute…
KEGG ENZYME: 2.7.2.1
Entry EC 2.7.2.1 Enzyme Name acetate kinase;acetokinase;AckA;AK;acetic kinase;acetate kinase (phosphorylating) Class Transferases;Transferring phosphorus-containing groups;Phosphotransferases with a carboxy group as acceptorBRITE hierarchy Sysname ATP:acetate phosphotransferase Reaction(IUBMB) ATP + acetate = ADP + acetyl phosphate [RN:R00315] Reaction(KEGG) Substrate Product Comment Requires Mg2+ for activity. While purified enzyme from Escherichia coli is specific for acetate…
KEGG COMPOUND: C00247
KEGG COMPOUND: C00247 COMPOUND: C00247 Help Entry C00247 Compound Name L-Sorbose;L-xylo-Hexulose Formula C6H12O6 Exact mass 180.0634 Mol weight 180.1559 Structure Mol fileKCF fileDB search Comment Reaction Pathway map00051 Fructose and mannose metabolism Enzyme Brite Compounds with biological roles [BR:br08001] Carbohydrates Monosaccharides Ketoses C00247 L-Sorbose BRITE hierarchy Other DBs KCF data Show ATOM 12 1 C1z C 26.2968 -14.4371 2 C1y C 26.2968 -15.8376 3 O2x O 25.0888 -13.7368 4 C1b…
Exosomal microRNA-618 derived from mesenchymal stem cells attenuate the progression of hepatic fibrosis by targeting Smad4
Introduction Hepatic fibrosis (HF) is a pathological phenomenon produced in the process of long-term damage and repair in the liver [1,2]. During the formation of HF, hepatocytes are damaged by various factors, such as chronic liver disease, and excessive intake of alcohol, and secrete a variety of cytokines [3]. Subsequently,…
Comprehensive bioinformatics analysis reveals the hub genes and pathways associated with multiple myeloma
This article was originally published here Hematology. 2022 Dec;27(1):280-292. doi: 10.1080/16078454.2022.2040123. ABSTRACT PURPOSE: While the prognosis of multiple myeloma (MM) has significantly improved over the last decade because of new treatment options, it remains incurable. Aetiological explanations and biological targets based on genomics may provide additional help for rational disease…
Validation of hub genes in acute pancreatitis
Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…
KEGG COMPOUND: C21620
KEGG COMPOUND: C21620 COMPOUND: C21620 Help Entry C21620 Compound Name S-[(E)-N-Hydroxy(indol-3-yl)acetimidoyl]-L-glutathione Formula C20H25N5O7S Exact mass 479.1475 Mol weight 479.5068 Structure Mol fileKCF fileDB search Reaction Enzyme Other DBs KCF data Show ATOM 33 1 C8y C 17.0403 -15.7134 2 C8y C 18.3672 -15.9928 3 C8y C 16.3420 -16.9006 4 C8x C 16.3420 -14.4564 5 C8x C 18.4371 -17.3895 6 N4x N 17.1800 -17.9482 7 C8x C 14.8754 -16.9006 8 C8x C 14.9452 -14.4564 9 C8x C 14.1770 -15.7134 10 O1b O 19.6829 -18.0281 11 N2b N 20.8589 -17.2684 12 C2c C 20.7891 -15.8717 13 C1b C 19.5432 -15.2331 14 C1b C 23.2109 -15.7506 15 S2a S 21.9650 -15.1120 16 C1c C 24.3869 -14.9909 17 N1b N 24.3170 -13.5927 18 C5a C 25.6328 -15.6295 19 O5a…
Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis
INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…
Fatty infiltration after rotator cuff tear
Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…
KEGG T03334: R50912_07385
Entry R50912_23945 CDS T03334 Name (GenBank) alpha-galactosidase KO K07407 alpha-galactosidase [EC:3.2.1.22] Organism paeq Paenibacillus sp. FSL R5-0912 Pathway paeq00052 Galactose metabolism paeq00561 Glycerolipid metabolism paeq00600 Sphingolipid metabolism paeq01100 Metabolic pathways Brite KEGG Orthology (KO) [BR:paeq00001] 09100 Metabolism 09101 Carbohydrate metabolism 00052 Galactose metabolism R50912_23945 09103 Lipid metabolism 00561 Glycerolipid metabolism R50912_23945 00600 Sphingolipid metabolism R50912_23945Enzymes [BR:paeq01000] 3. Hydrolases 3.2 Glycosylases 3.2.1 Glycosidases, i.e. enzymes that hydrolyse O-…
KEGG ENZYME: 2.4.1.81
Entry EC 2.4.1.81 Enzyme Name flavone 7-O-beta-glucosyltransferase;UDP-glucose-apigenin beta-glucosyltransferase;UDP-glucose-luteolin beta-D-glucosyltransferase;uridine diphosphoglucose-luteolin glucosyltransferase;uridine diphosphoglucose-apigenin 7-O-glucosyltransferase;UDP-glucosyltransferase (ambiguous) Class Transferases;Glycosyltransferases;HexosyltransferasesBRITE hierarchy Sysname UDP-glucose:5,7,3′,4′-tetrahydroxyflavone 7-O-beta-D-glucosyltransferase Reaction(IUBMB) UDP-glucose + 5,7,3′,4′-tetrahydroxyflavone = UDP + 7-O-beta-D-glucosyl-5,7,3′,4′-tetrahydroxyflavone [RN:R03588] Reaction(KEGG) Substrate UDP-glucose [CPD:C00029]; 5,7,3′,4′-tetrahydroxyflavone [CPD:C01514] Product UDP [CPD:C00015]; 7-O-beta-D-glucosyl-5,7,3′,4′-tetrahydroxyflavone [CPD:C03951] Comment A number of flavones, flavanones and flavonols can function as acceptors….
KEGG REACTION: R02703
KEGG REACTION: R02703 REACTION: R02703 Help Entry R02703 Reaction Name D-Mannitol-1-phosphate:NAD+ 5-oxidoreductase Definition D-Mannitol 1-phosphate + NAD+ <=> beta-D-Fructose 6-phosphate + NADH + H+ Equation Reaction class Enzyme Pathway rn00051 Fructose and mannose metabolism Orthology LinkDB All DBs DBGET integrated database retrieval system Read more here: Source link
KEGG ENZYME: 2.2.1.4
KEGG ENZYME: 2.2.1.4 ENZYME: 2.2.1.4 Help Entry EC 2.2.1.4 Enzyme Name acetoin—ribose-5-phosphate transaldolase;1-deoxy-D-altro-heptulose-7-phosphate synthetase;1-deoxy-D-altro-heptulose-7-phosphate synthase;3-hydroxybutan-2-one:D-ribose-5-phosphate aldehydetransferase [wrong substrate name] Class Transferases;Transferring aldehyde or ketonic groups;Transketolases and transaldolasesBRITE hierarchy Sysname 3-hydroxybutan-2-one:D-ribose-5-phosphate aldehydetransferase Reaction(IUBMB) 3-hydroxybutan-2-one + D-ribose 5-phosphate = acetaldehyde + 1-deoxy-D-altro-heptulose 7-phosphate [RN:R02345] Reaction(KEGG) Substrate 3-hydroxybutan-2-one [CPD:C00466]; D-ribose 5-phosphate [CPD:C00117] Product acetaldehyde…
KEGG REACTION: R03385
KEGG REACTION: R03385 REACTION: R03385 Help Entry R03385 Reaction Name 3-hydroxy-2-methylpyridine-5-carboxylate,NADH:oxygen oxidoreductase (ring-opening) Definition 3-Hydroxy-2-methylpyridine-5-carboxylate + Oxygen + NADH + H+ <=> 2-(Acetamidomethylene)succinate + NAD+ Equation Comment Reaction class Enzyme Pathway rn01120 Microbial metabolism in diverse environments Orthology Other DBs LinkDB All DBs DBGET integrated database retrieval system Read more…
KEGG COMPOUND: C06070
KEGG COMPOUND: C06070 COMPOUND: C06070 Help Entry C06070 Compound Name Iridotrial;(1S,2R,3S)-2-Formyl-alpha-(hydroxymethylene)-3-methylcyclopentaneacetaldehyde Formula C10H14O3 Exact mass 182.0943 Mol weight 182.2164 Structure Mol fileKCF fileDB search Reaction Pathway map01110 Biosynthesis of secondary metabolites Enzyme Brite Lipids [BR:br08002] PR Prenol lipids PR01 Isoprenoids PR0102 C10 isoprenoids (monoterpenes) PR010207 Iridoid, 10-alkyliridoid and secoiridoid monoterpenoids C06070 IridotrialPhytochemical compounds [BR:br08003] Terpenoids Monoterpenoids (C10) Iridoids C06070 Iridotrial BRITE hierarchy…
Comprehensive circRNA Analyses in Human Vertebrae of GIOP and Its Molecular Mechanism
Circular RNAs (circRNAs) are a novel class of noncoding RNAs that play important roles in human diseases. However, the regulation of circRNAs in glucocorticoid-induced osteoporosis (GIOP) has not been reported. In this study, we performed high-throughput sequencing to identify altered circRNAs in the vertebrae from GIOP patients. A total of…
Identification of a four-gene signature & PTC.
Introduction Thyroid carcinoma (THCA) is the most common type of endocrine malignancy and its incidence is increasing.1 Based on its histopathological characteristics, thyroid carcinoma can be classified into multiple subtypes, such as papillary thyroid carcinoma (PTC), follicular thyroid carcinoma, and anaplastic thyroid carcinoma.2 PTC is the most common subtype of…
How to do functional analysis on differentially expressed gene list from RNA-seq data?
How to do functional analysis on differentially expressed gene list from RNA-seq data? 0 @06f08eeb Last seen 1 day ago Canada Hi all, I am a complete beginner in terms of bioinformatics analysis and I am hoping to complete some functional analysis on some differentially expressed gene lists of some…
KEGG REACTION: R00481
KEGG REACTION: R00481 REACTION: R00481 Help Entry R00481 Reaction Name L-aspartate:oxygen oxidoreductase Definition L-Aspartate + Oxygen <=> Iminoaspartate + Hydrogen peroxide Equation Comment Reaction class Enzyme Pathway rn00760 Nicotinate and nicotinamide metabolism rn01240 Biosynthesis of cofactors Module M00115 NAD biosynthesis, aspartate => quinolinate => NAD Orthology Other DBs LinkDB All…
Novel diagnostic biomarkers for keloid based on GEO database
Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…
KEGG T00007: b1542
Entry b4323 CDS T00007 Symbol uxuB Name (RefSeq) D-mannonate oxidoreductase KO K00040 fructuronate reductase [EC:1.1.1.57] Organism eco Escherichia coli K-12 MG1655 Pathway eco00040 Pentose and glucuronate interconversions eco01100 Metabolic pathways Module eco_M00061 D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P Brite KEGG Orthology (KO) [BR:eco00001] 09100 Metabolism 09101 Carbohydrate metabolism 00040 Pentose and glucuronate interconversions b4323 (uxuB)Enzymes…
KEGG REACTION: R00226
Entry R00226 Reaction Name pyruvate:pyruvate acetaldehydetransferase (decarboxylating);(S)-2-acetolactate pyruvate-lyase (carboxylating) Definition (S)-2-Acetolactate + CO2 <=> 2 Pyruvate Equation Comment Reaction class Enzyme Pathway rn00290 Valine, leucine and isoleucine biosynthesis rn00660 C5-Branched dibasic acid metabolism rn00770 Pantothenate and CoA biosynthesis rn01110 Biosynthesis of secondary metabolites rn01210 2-Oxocarboxylic acid metabolism rn01230 Biosynthesis of amino…
Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells
Aghamohseni H, Ohadi K, Spearman M, Krahn N, Moo-Young M, Scharer JM, Butler M, Budman HM (2014) Effects of nutrient levels and average culture pH on the glycosylation pattern of camelid-humanized monoclonal antibody. J Biotechnol 186:98–109. doi.org/10.1016/j.jbiotec.2014.05.024 CAS Article PubMed Google Scholar Altamirano C, Illanes A, Casablancas A, Gámez X,…
KEGG ENZYME: 3.1.3.96
Entry EC 3.1.3.96 Enzyme Name pseudouridine 5′-phosphatase;pseudouridine 5′-monophosphatase;5′-PsiMPase;HDHD1 Class Hydrolases;Acting on ester bonds;Phosphoric-monoester hydrolasesBRITE hierarchy Sysname pseudouridine 5′-phosphohydrolase Reaction(IUBMB) pseudouridine 5′-phosphate + H2O = pseudouridine + phosphate [RN:R11180] Reaction(KEGG) R11180 Reaction Substrate pseudouridine 5′-phosphate [CPD:C01168]; H2O [CPD:C00001] Product pseudouridine [CPD:C02067]; phosphate [CPD:C00009] Comment Requires Mg2+ for activity. History EC 3.1.3.96 created 2014…
KEGG REACTION: R03197
REACTION: R03197 Help Entry R03197 Reaction Name Uroporphyrinogen-III carboxy-lyase Definition Uroporphyrinogen III <=> Coproporphyrinogen III + 4 CO2 Equation Reaction class Enzyme Pathway rn01110 Biosynthesis of secondary metabolites rn01240 Biosynthesis of cofactors Module M00121 Heme biosynthesis, plants and bacteria, glutamate => heme M00868 Heme biosynthesis, animals and fungi, glycine =>…
KEGG PATHWAY: map00051
Entry map00051 Pathway Name Fructose and mannose metabolism Class Metabolism; Carbohydrate metabolismBRITE hierarchy Pathway map map00051 Fructose and mannose metabolism Ortholog table Module M00114 Ascorbate biosynthesis, plants, fructose-6P => ascorbate [PATH:map00051] Other DBs Relatedpathway map00010 Glycolysis / Gluconeogenesis map00053 Ascorbate and aldarate metabolism map00520 Amino sugar and nucleotide sugar metabolism KO pathway Read…
KEGG ENZYME: 6.5.1.9
Entry EC 6.5.1.9 Enzyme Name cyclic 2,3-diphosphoglycerate synthase;cpgS (gene name) Class Ligases;Forming phosphoric-ester bonds;Ligases that form phosphoric-ester bonds (only sub-subclass identified to date)BRITE hierarchy Sysname (2R)-2,3-bisphosphoglycerate ligase (cyclizing) Reaction(IUBMB) ATP + 2,3-diphospho-D-glycerate = ADP + phosphate + cyclic 2,3-bisphosphoglycerate [RN:R03298] Reaction(KEGG) Substrate Product Comment The enzyme is present in a number of…
Immune-related Prognostic Genes of ccRCC
Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…
KEGG REACTION: R00750
Entry R00750 Reaction Name 4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming) Definition Acetaldehyde + Pyruvate <=> 4-Hydroxy-2-oxopentanoate Equation Reaction class Enzyme Pathway rn00360 Phenylalanine metabolism rn01120 Microbial metabolism in diverse environments rn01220 Degradation of aromatic compounds Module M00545 Trans-cinnamate degradation, trans-cinnamate => acetyl-CoA M00569 Catechol meta-cleavage, catechol => acetyl-CoA / 4-methylcatechol => propanoyl-CoA Orthology Other…
Identification of differentially expressed genes in AF
Defeng Pan,1,* Yufei Zhou,2,* Shengjue Xiao,1,* Yue Hu,3,* Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…
Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr
Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…
KEGG ORTHOLOGY: K11868
KEGG ORTHOLOGY: K11868 ORTHOLOGY: K11868 Help Entry K11868 KO Symbol CYP71A13 Name indoleacetaldoxime dehydratase [EC:4.8.1.3] Pathway Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism 09105 Amino acid metabolism 00380 Tryptophan metabolism K11868 CYP71A13; indoleacetaldoxime dehydratase 09180 Brite Hierarchies 09181 Protein families: metabolism 00199 Cytochrome P450 K11868 CYP71A13; indoleacetaldoxime dehydrataseEnzymes [BR:ko01000] 4. Lyases 4.8 Nitrogen-oxygen lyases 4.8.1 Hydro-lyases 4.8.1.3 indoleacetaldoxime dehydratase K11868 CYP71A13; indoleacetaldoxime dehydrataseCytochrome P450 [BR:ko00199] Cytochrome P450, plant type CYP71 family K11868 CYP71A13;…
biopython – Github Help
1 1 0 biopython,How to rescue failed project ? To do: 1. The wrapper of the KEGG gene orthology database should obtain gene names. 2. Pandas should be replaced by other software more appropriate for data mining by counting lines in tables ( see towardsdatascience.com/surprising-sorting-tips-for-data-scientists-9c360776d7e). i User: dariusz-izak-doktorat pandas python…
KEGG ENZYME: 2.2.1.10
Entry EC 2.2.1.10 Enzyme Name 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase;ADH synthase;ADHS;MJ0400 (gene name) Class Transferases;Transferring aldehyde or ketonic groups;Transketolases and transaldolasesBRITE hierarchy Sysname L-aspartate 4-semialdehyde:1-deoxy-D-threo-hexo-2,5-diulose 6-phosphate methylglyoxaltransferase Reaction(IUBMB) L-aspartate 4-semialdehyde + 1-deoxy-D-threo-hexo-2,5-diulose 6-phosphate = 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate + 2,3-dioxopropyl phosphate [RN:R08568] Reaction(KEGG) Substrate L-aspartate 4-semialdehyde [CPD:C00441]; 1-deoxy-D-threo-hexo-2,5-diulose 6-phosphate [CPD:C16848] Product 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate; 2,3-dioxopropyl phosphate [CPD:C16849] Comment The enzyme…
KEGG T01005: 453503
Entry 453503 CDS T01005 Symbol SNX1 Name (RefSeq) sorting nexin-1 isoform X3 KO K17917 sorting nexin-1/2 Organism ptr Pan troglodytes (chimpanzee) Pathway ptr04144 Endocytosis Brite KEGG Orthology (KO) [BR:ptr00001] 09140 Cellular Processes 09141 Transport and catabolism 04144 Endocytosis 453503 (SNX1) 09180 Brite Hierarchies 09182 Protein families: genetic information processing 04131 Membrane trafficking [BR:ptr04131] 453503 (SNX1) 09183 Protein families: signaling and cellular processes 04990…
kegg – Github Help
1 1 0 kegg,How to rescue failed project ? To do: 1. The wrapper of the KEGG gene orthology database should obtain gene names. 2. Pandas should be replaced by other software more appropriate for data mining by counting lines in tables ( see towardsdatascience.com/surprising-sorting-tips-for-data-scientists-9c360776d7e). i User: dariusz-izak-doktorat pandas python…
Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet
1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS PubMed PubMed Central Google Scholar 2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …
Sod1 integrates oxygen availability to redox regulate NADPH production and the thiol redoxome
Significance Cu/Zn superoxide dismutase (Sod1) is a key antioxidant enzyme, and its importance is underscored by the fact that its ablation in cell and animal models results in oxidative stress; metabolic defects; and reductions in cell proliferation, viability, and lifespan. Curiously, Sod1 detoxifies superoxide radicals (O2•−) in a manner that…
KEGG COMPOUND: C09877
KEGG COMPOUND: C09877 COMPOUND: C09877 Help エントリ C09877 Compound 名称 (+)-β-フェランドレン;(+)-beta-Phellandrene 組成式 C10H16 質量 136.1252 分子量 136.234 構造式 Mol fileKCF fileDB search 階層分類 Lipids [BR:br08002] PR Prenol lipids PR01 Isoprenoids PR0102 C10 isoprenoids (monoterpenes) PR010209 Menthane monoterpenoids C09877 (+)-beta-PhellandrenePhytochemical compounds [BR:br08003] Terpenoids Monoterpenoids (C10) Cyclic monoterpenes C09877 (+)-beta-Phellandrene BRITE hierarchy リンク LinkDB All DBs » English version DBGET integrated database retrieval system…
KEGG ENZYME: 1.14.14.86
Entry EC 1.14.14.86 Enzyme Name ent-kaurene monooxygenase;ent-kaurene oxidase (misleading) Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donorBRITE hierarchy Sysname ent-kaur-16-ene,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (hydroxylating) Reaction(IUBMB) ent-kaur-16-ene + 3 [reduced NADPH—hemoprotein…
KEGG REACTION: R01800
Entry R01800 Reaction Name CDP-diacylglycerol:L-serine 3-phosphatidyltransferase Definition CDP-diacylglycerol + L-Serine <=> CMP + Phosphatidylserine Equation Reaction class Enzyme Pathway rn00260 Glycine, serine and threonine metabolism rn00564 Glycerophospholipid metabolism rn01110 Biosynthesis of secondary metabolites Module M00093 Phosphatidylethanolamine (PE) biosynthesis, PA => PS => PE Orthology K00998 CDP-diacylglycerol—serine O-phosphatidyltransferase [EC:2.7.8.8] K17103 CDP-diacylglycerol—serine O-phosphatidyltransferase…
KEGG ORTHOLOGY: K02207
Brite KEGG Orthology (KO) [BR:ko00001] 09120 Genetic Information Processing 09123 Folding, sorting and degradation 04120 Ubiquitin mediated proteolysis K02207 UBE2R, UBC3, CDC34; ubiquitin-conjugating enzyme E2 R 09180 Brite Hierarchies 09182 Protein families: genetic information processing 04121 Ubiquitin system K02207 UBE2R, UBC3, CDC34; ubiquitin-conjugating enzyme E2 REnzymes [BR:ko01000] 2. Transferases 2.3 Acyltransferases 2.3.2 Aminoacyltransferases 2.3.2.23 E2 ubiquitin-conjugating enzyme K02207 UBE2R, UBC3, CDC34; ubiquitin-conjugating enzyme E2 RUbiquitin system [BR:ko04121] Ubiquitin-conjugating enzymes (E2) Ubiquitin-conjugating…
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions
1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS PubMed Google Scholar 3. Oh, J. et al. Temporal stability…
Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice
O304 treatment prevents islet gene expression signature changes induced by HFD We have previously demonstrated that the AMPK activator O304 improves blood glucose homeostasis in both human T2D subjects as well as in high-fat diet induced obese and diabetic mouse models. In the present study, we have now analysed the…
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics
1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article Google Scholar 2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…
KEGG ENZYME: 6.3.1.17
KEGG ENZYME: 6.3.1.17 ENZYME: 6.3.1.17 Help Entry EC 6.3.1.17 Enzyme Name beta-citrylglutamate synthase;NAAG synthetase I;NAAGS-I;RIMKLB (gene name) (ambiguous) Class Ligases;Forming carbon-nitrogen bonds;Acid-D-ammonia (or amine) ligases (amide synthases)BRITE hierarchy Sysname citrate:L-glutamate ligase (ADP-forming) Reaction(IUBMB) ATP + citrate + L-glutamate = ADP + phosphate + beta-citryl-L-glutamate [RN:R10677] Reaction(KEGG) Substrate Product Comment The enzyme,…
Crosstalk between Venous Thromboembolism and Periodontal Diseases: A Bioinformatics Analysis
This article was originally published here Dis Markers. 2021 Dec 10;2021:1776567. doi: 10.1155/2021/1776567. eCollection 2021. ABSTRACT BACKGROUND: This current study applied bioinformatics analysis to reveal the crosstalk between venous thromboembolism (VTE) and periodontitis, as well as the potential role of immune-related genes in this context. METHODS: Expression data were downloaded…
KEGG COMPOUND: C20284
KEGG COMPOUND: C20284 COMPOUND: C20284 Help Entry C20284 Compound Name Benzenediazonium;Benzenediazonium ion Formula C6H5N2 Exact mass 105.0453 Mol weight 105.1173 Structure Mol fileKCF fileDB search Pathway map05204 Chemical carcinogenesis – DNA adducts Other DBs LinkDB All DBs KCF data Show ATOM 8 1 C8y C 18.6066 -15.8364 2 C8x C 17.4048 -16.5269 3 C8x C 19.8279 -16.5269 4 N3a N 18.6003 -14.4425 #+ 5 C8x C 17.4048 -17.9334 6 C8x C 19.8279 -17.9334 7 N3a N 20.3623 -13.3957 8 C8x C 18.6066 -18.6494BOND 8 1 1 2…
Adrenal aldosterone-producing adenoma | IJGM
Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…
Establishment of sunitinib-resistant CDX model of ccRCC
Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…
KEGG REACTION: R01918
KEGG REACTION: R01918 REACTION: R01918 Help Entry R01918 Reaction Name gamma-L-glutamyl-L-cysteinyl-glycine:spermidine amidase Definition Glutathionylspermidine + H2O <=> Glutathione + Spermidine Equation Reaction class Enzyme Pathway Orthology Other DBs LinkDB All DBs DBGET integrated database retrieval system Read more here: Source link
KEGG COMPOUND: C20288
KEGG COMPOUND: C20288 COMPOUND: C20288 Help Entry C20288 Compound Name Formula C13H12N4O4S Exact mass 320.0579 Mol weight 320.3238 Structure Mol fileKCF fileDB search Pathway map05204 Chemical carcinogenesis – DNA adducts Other DBs LinkDB All DBs KCF data Show ATOM 22 1 C8y C 17.1244 -16.4935 2 C8x C 17.1244 -17.8970 3 N5x N 18.3400 -18.5988 4 C8y C 19.5556 -17.8970 5 C8y C 19.5556 -16.4935 6 C8x C 18.3400 -15.7917 7 N5x N 20.8905 -18.3308 8 C8y C 21.7155 -17.1953 9 N4y N 20.8905 -16.0597 10 C8y C 15.9089 -15.7917 11 C8x C 15.9089 -14.3883 12 C8x…
KEGG COMPOUND: C21642
KEGG COMPOUND: C21642 COMPOUND: C21642 Help Entry C21642 Compound Name 4-Hydroxynonenal;4-Hydroxy-2-nonenal;4-HNE Formula C9H16O2 Exact mass 156.115 Mol weight 156.2221 Structure Mol fileKCF fileDB search Pathway Other DBs LinkDB All DBs KCF data Show ATOM 11 1 C1a C 13.1567 -15.1124 2 C1b C 14.3460 -15.8120 3 C1b C 15.6053 -15.1124 4 C1b C 16.7947 -15.8120 5 C1b C 17.9840 -15.1124 6 C1c C 19.2433 -15.8120 7 C2b C 20.4326 -15.1124 8 C2b C 21.6219 -15.8120 9 C4a C 22.8812 -15.1124 10 O4a O 24.0706 -15.8120 11 O1a O 19.2433 -17.2112BOND 10 1 1 2 1 2 2 3 1 3 3 4 1 4 4 5 1 5 5 6 1 6 6 7…
Prognosis Biomarkers via WGCNA in HCC
Introduction According to the cancer statistics reported in 2020, hepatocellular carcinoma (HCC) is the main type of Primary Carcinoma of the Liver and the second leading causes of cancer-related death globally, with a five-year survival rate < 20%.1 Currently, surgical resection, a standard therapy for HCC, contributes to the prognosis…
KEGG PATHWAY: Diterpenoid biosynthesis – Oryza sativa japonica (Japanese rice) (RefSeq)
Complete onlyIncluding 1 block missingIncluding any incomplete Pathway modules Biosynthesis of terpenoids and polyketides Plant terpenoid biosynthesis M00927 Gibberellin A12 biosynthesis M00928 Gibberellin A4/A1 biosynthesis M00929 Gibberellin A1 biosynthesis Read more here: Source link
KEGG PATHWAY: Benzoxazinoid biosynthesis – Oryza sativa japonica (Japanese rice) (RefSeq)
KEGG PATHWAY: Benzoxazinoid biosynthesis – Oryza sativa japonica (Japanese rice) (RefSeq) [ | Pathway entry | Download KGML | Show description | Image (png) file | Help ] Benzoxazinoids (hydroxamic acids) are plant secondary metabolites that serve as important factors for host resistance against microbial pathogens and insects and for…
KEGG ENZYME: 2.3.1.68
Entry EC 2.3.1.68 Enzyme Name glutamine N-acyltransferase Class Transferases;Acyltransferases;Transferring groups other than aminoacyl groupsBRITE hierarchy Sysname acyl-CoA:L-glutamine N-acyltransferase Reaction(IUBMB) acyl-CoA + L-glutamine = CoA + N-acyl-L-glutamine [RN:R00577] Reaction(KEGG) R00577 Reaction Substrate acyl-CoA [CPD:C00040]; L-glutamine [CPD:C00064] Product CoA [CPD:C00010]; N-acyl-L-glutamine [CPD:C02716] Comment Phenylacetyl-CoA and (indol-3-yl)acetyl-CoA, but not benzoyl-CoA, can act as acyl donors….
KEGG ENZYME: 4.1.1.65
Entry EC 4.1.1.65 Enzyme Name phosphatidylserine decarboxylase;PS decarboxylase;phosphatidyl-L-serine carboxy-lyase Class Lyases;Carbon-carbon lyases;Carboxy-lyasesBRITE hierarchy Sysname phosphatidyl-L-serine carboxy-lyase (phosphatidylethanolamine-forming) Reaction(IUBMB) phosphatidyl-L-serine = phosphatidylethanolamine + CO2 [RN:R02055] Reaction(KEGG) Substrate phosphatidyl-L-serine [CPD:C02737] Product Comment A pyridoxal-phosphate protein. In Escherichia coli, the prosthetic group is a pyruvoyl group. History EC 4.1.1.65 created 1976 Pathway ec00564 Glycerophospholipid metabolism…
Get data from KEGG Brite
Get data from KEGG Brite 0 Hi, I would like to retrieve all the interactions between ligands and target proteins from the KEGG BRITE database. Ideally, each entry will contain a protein name, a list of interacting ligands, its FASTA sequence and an sdf or mol2 coordinates of the ligand,…
KEGG PATHWAY: Fluorobenzoate degradation – Escherichia coli K-12 MG1655
[ Pathway menu | Pathway entry | Download KGML | Image (png) file | Help ] Option Scale: 100% Search ID search Color Read more here: Source link
Metabolite label to KEGG Id
Metabolite label to KEGG Id 0 Hi! I have a list of metabolite labels with associated values (metabolite A has been found in sample 1), as follows: metabolite_label value Total_C 4.605948787 non_HDL_C 3.598204496 Remnant_C 1.571938945 VLDL_C 0.808513241 Clinical_LDL_C 2.868314163 I want to use the Omu R package to do some…
KEGG PATHWAY: DNA replication – Escherichia coli K-12 MG1655
KEGG PATHWAY: DNA replication – Escherichia coli K-12 MG1655 [ | Pathway entry | Download KGML | Show description | Image (png) file | Help ] A complex network of interacting proteins and enzymes is required for DNA replication. Generally, DNA replication follows a multistep enzymatic pathway. At the DNA…
KEGG PATHWAY: Riboflavin metabolism – Oryza sativa japonica (Japanese rice) (RefSeq)
Complete onlyIncluding 1 block missingIncluding any incomplete Pathway modules Metabolism of cofactors and vitamins Cofactor and vitamin metabolism M00125 Riboflavin biosynthesis, plants and bacteria M00911 Riboflavin biosynthesis, fungi Read more here: Source link
Identification of Hub Genes in Patients with Alzheimer Disease and Obs
Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…
Identification of lipid metabolism-associated gene signature
Background Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer. Despite the dramatic improvement in breast cancer prognosis due to recent therapeutic advances, such as more effective adjuvant and neo-adjuvant chemotherapies, together with more radical and safer surgery, advances in early diagnosis and treatment over the…
KEGG PATHWAY: Other glycan degradation
[ Pathway menu | Pathway entry | Download KGML | Image (png) file | Help ] Option Scale: 100% Search ID search Color Read more here: Source link
KEGG COMPOUND: C00766
KEGG COMPOUND: C00766 COMPOUND: C00766 Help Entry C00766 Compound Name Flavanone;2,3-Dihydroflavone Formula C15H12O2 Exact mass 224.0837 Mol weight 224.2546 Structure Mol fileKCF fileDB search Comment Generic compound in reaction hierarchy Reaction Pathway map01060 Biosynthesis of plant secondary metabolites Enzyme Other DBs KCF data Show ATOM 17 1 C8x C 7.7700 -25.2700 2 C8x C 7.7700 -26.6700 3 C8x C 8.9824 -27.3700 4 C8y C 10.1949 -26.6700 5 C8y C 10.1949 -25.2700 6 C8x…
Parallel genomic responses to historical climate change and high elevation in East Asian songbirds
Extreme environments present profound physiological stress. The adaptation of closely related species to these environments is likely to invoke congruent genetic responses resulting in similar physiological and/or morphological adaptations, a process termed “parallel evolution” (1). Existing evidence shows that parallel evolution is more common at the phenotypic level than at…
KEGG PATHWAY: beta-Lactam resistance – Escherichia coli K-12 MG1655
KEGG PATHWAY: beta-Lactam resistance – Escherichia coli K-12 MG1655 [ | Pathway entry | Download KGML | Show description | Image (png) file | Help ] The beta-lactam antibiotics are the most widely used group of antibiotics, which exert their effect by interfering with the structural crosslinking of peptidoglycans in…
Index of /~psgendb/doc/local/zhangju/eclipse_project/Pl_MGCB2/Module_Dir
Name Last modified Size Description Parent Directory – Cazy_gbk_protein.pl 2015-11-09 14:56 2.5K DataRetrieving.pl 2015-11-09 14:56 6.7K GOshell.pl 2015-11-09 14:56 24K ParseGffFile.pl 2015-11-09 14:56 17K ParseKEGG.pl 2015-11-09 14:56 17K Parse_Fasta.pl 2015-11-09 14:56 34K Parse_Fastq.pl 2015-11-09 14:56 1.2K Parse_Genbank.pl 2015-11-09 14:56 86K …
KEGG COMPOUND: C21825
KEGG COMPOUND: C21825 COMPOUND: C21825 Help Entry C21825 Compound Name 9beta-Pimara-7,15-diene-3beta-ol Formula C20H32O Exact mass 288.2453 Mol weight 288.4675 Structure Mol fileKCF fileDB search Reaction Pathway map01110 Biosynthesis of secondary metabolites Enzyme LinkDB All DBs KCF data Show ATOM 21 1 C1x C 14.9922 -16.1836 2 C1y C 14.9922 -17.5848 3 C1z C 16.1832 -18.2854 4 C1y C 17.4442 -17.5848 5 C1z C 17.4442 -16.1836 6 C1x C 16.1832 -15.4830 7 C1x C 18.6352 -18.2854 8 C2x C 19.8262 -17.5848 9 C2y C 19.8262 -16.1836 10 C1y C 18.6352 -15.4830 11 C1x C 21.0873 -15.4830 12 C1z…